Biological Phenomena, Cell Phenomena, and Immunity Commons^™

Distinct Transcriptome Profiles Of Gag-Specific Cd8+ T Cells Temporally Correlated With The Protection Elicited By Sivδnef Live Attenuated Vaccine, Wuxun Lu, Yanmin Wu, Fangrui Ma, R. Paul Johnson, Qingsheng Li

Nebraska Center for Virology: Faculty Publications

The live attenuated vaccine (LAV) SIVmac239Δnef (SIVΔnef) confers the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. This vaccine has a unique feature of time-dependent protection: macaques are not protected at 3±5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. Although the exact mechanisms of the time-dependent protection remain incompletely understood, studies suggested that both cellular and humoral immunities contribute to this time-dependent protection. To further elucidate the mechanisms of protection induced by SIVΔnef, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) …

Chloroviruses Have A Sweet Tooth, James L. Van Etten, Irina V. Agarkova, David D. Dunigan, Michela Tonetti, Cristina De Castro, Garry A. Duncan

Nebraska Center for Virology: Faculty Publications

Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins involved in manipulating carbohydrates. These include enzymes involved in making extracellular polysaccharides, such as hyaluronan and chitin, enzymes that make nucleotide sugars, such as GDP-L-fucose and GDP-D-rhamnose and enzymes involved in the synthesis of glycans attached to the virus major capsid proteins. This latter process differs from that of all other glycoprotein containing viruses that traditionally use …

Tryptophan 375 Stabilizes The Outer-Domain Core Of Gp120 For Hiv Vaccine Immunogen Design, Duoyi Hu, Dane Bowder, Wenzhong Wei, Jesse Thompson, Mark A. Wilson, Shi-Hua Xiang

Nebraska Center for Virology: Faculty Publications

The outer-domain core of gp120 may serve as a better HIV vaccine immunogen than the full-length gp120 because of its greater stability and immunogenicity. In our previous report, we introduced two disulfide bonds to the outer-domain core of gp120 to fix its conformation into a CD4-bound state, which resulted in a significant increase in its immunogenicity when compared to the wild-type outer-domain core. In this report, to further improve the immunogenicity of the outer-domain core based immunogen, we have introduced a Tryptophan residue at gp120 amino acid sequence position 375 (375S/W). Our data from immunized guinea pigs indeed shows a …

Preferential Lineage-Specific Differentiation Of Osteoblast-Derived Induced Pluripotent Stem Cells Into Osteoprogenitors, Casey L. Roberts, Silvia S. Chen, Angela C. Murchison, Rebecca A. Ogle, Michael P. Francis, Roy C. Ogle, Patrick C. Sachs

School of Medical Diagnostics & Translational Sciences Publications

While induced pluripotent stem cells (iPSCs) hold great clinical promise, one hurdle that remains is the existence of a parental germ-layer memory in reprogrammed cells leading to preferential differentiation fates. While it is problematic for generating cells vastly different from the reprogrammed cells' origins, it could be advantageous for the reliable generation of germ-layer specific cell types for future therapeutic use. Here we use human osteoblast-derived iPSCs (hOB-iPSCs) to generate induced osteoprogenitors (iOPs). Osteoblasts were successfully reprogrammed and demonstrated by endogenous upregulation of Oct4, Sox2, Nanog, TRA-1-81, TRA-16-1, SSEA3, and confirmatory hPSC Scorecard Algorithmic Assessment. The hOB-iPSCs formed embryoid bodies …

Characterization Of A New Chlorovirus Type With Permissive And Non-Permissive Features On Phylogenetically Related Algal Strains, Cristian F. Quispe, Ahmed Esmael, Olivia Sonderman, Michelle Mcquinn, Irina Agarkova, Mohammed Battah, Garry A. Duncan, David D. Dunigan, Timothy P. L. Smith, Cristina Decastro, Immacolata Speciale, Fangrui Ma, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

A previous report indicated that prototype chlorovirus PBCV-1 replicated in two Chlorella variabilis algal strains, NC64A and Syngen 2-3, that are ex-endosymbionts isolated from the protozoan Paramecium bursaria. Surprisingly, plaque-forming viruses on Syngen 2-3 lawns were often higher than on NC64A lawns from indigenous water samples. These differences led to the discovery of viruses that exclusively replicate in Syngen 2-3 cells, named Only Syngen (OSy) viruses. OSy-NE5, the prototype virus for the proposed new species, had a linear dsDNA genome of 327 kb with 44-nucleotide-long, incompletely base-paired, covalently closed hairpin ends. Each hairpin structure was followed by an identical …

Radioactive Contamination Of Natural Biological Systems: Oxidative Balance And Genetic Stability, Daniel Einor

Theses and Dissertations

The global demand for nuclear energy grows, and so do the risks of an accidental release of nuclear products into the environment. Therefore, understanding the health and ecological effects of contamination by radionuclides should be of great interest for biomedical specialists and the public. Empirical studies unequivocally show that high doses of ionizing radiation (IR) shift the redox-balance of many biological systems and increase the rates of genetic errors. However, the effects of chronic low doses of radiation vary significantly between tissues and between species. The present dissertation comprises the results of experimental and meta-analytical research of a variety of …

Visualizing Morphogenesis With The Processing Programming Language, Avik Patel, Amar Bains, Richard Millet, Tamira Elul

Faculty Publications & Research of the TUC College of Osteopathic Medicine

We used Processing, a visual artists’ programming language developed at MIT Media Lab, to simulate cellular mechanisms of morphogenesis – the generation of form and shape in embryonic tissues. Based on observations of in vivo time-lapse image sequences, we created animations of neural cell motility responsible for elongating the spinal cord, and of optic axon branching dynamics that establish primary visual connectivity. These visual models underscore the significance of the computational decomposition of cellular dynamics underlying morphogenesis.

Reactivation Of Hiv-1 Proviruses In Immune-Compromised Mice Engrafted With Human Voa-Negative Cd4+ T Cells, Zhe Yuan, Guobin Kang, Wuxun Lu, Qingsheng Li

Nebraska Center for Virology: Faculty Publications

Background: HIV-1 infection remains incurable on antiretroviral therapy (ART) due to virus latency. To date, enhanced co-culture assays, including viral outgrowth assays (VOA), are commonly used to measure HIV-1 latent reservoirs and evaluate latency-reversing agents (LRAs). However, VOA can only reactivate a small fraction of intact proviruses.

Methods: To explore the utility of NOD scid gamma (NSG) mice as an in vivo model to reactivate HIV-1 proviruses from VOA-negative CD4+ T cells, resting CD4+ T cells from an HIV-1 latently infected individual were isolated and the human CD4+ T cells corresponding to VOA-positive and VOA-negative CD4+ T cells were engrafted …

Environmental Relationships And Predator-Prey Interactions Within The Snapper-Grouper Complex In The Southeastern U.S. Atlantic – Implications For Fisheries Management, Dawn M. Glasgow

Theses and Dissertations

Stock assessments indicate many valuable fish species are declining, or are considered overfished and/or are undergoing overfishing. Fisheries scientists and managers in the southeastern U.S. typically have utilized a single-species approach, and relied on catch per unit effort data derived from fishery-independent surveys to determine indices of abundance for economically important reef fish. However, catchability for these surveys vary for many reasons including environmental and predator-prey relationships. This research was developed to elucidate environmental influences on reef fish assemblages and distribution of reef-associated marine predators, and examine predator-prey dynamics that may influence relative abundance of large predators based on chevron …

Applications Of Multimedia Resources Developed As Part Of The Virtual Cell Animation Collection In Undergraduate Introductory Biology, Eric Edward Goff

Theses and Dissertations

Calls for reform in undergraduate STEM education have arisen from an increased need for well-trained biology graduates in the future scientific workforce. To address this need, many institutions have focused on a pedagogical restructuring of instructional practices to promote deeper conceptual understanding of core biological concepts. This study investigates the implementation of multimedia resources as a possible reliable supplement to undergraduate introductory biology and aims to provide empirical evidence on the instructional best practices of their use. As a central part of this study, we focus on one specific multimedia package, the Virtual Cell Animation Collection, due to its developmental …

Modulation Of Pkr Activity During Hiv Infection And Cellular Stress By Pact And Trbp, Evelyn E. Chukwurah

Theses and Dissertations

A crucial component of the cellular response to stress is the attenuation of protein synthesis to allow the cell to dedicate resources for the restoration of homeostasis or towards the induction of apoptotic cell death in case the stressors overwhelm the cell. This process is itself regulated by one of the four eIF2α kinases of which PKR (Protein Kinase R) is responsible for inhibiting general translation during viral infection, oxidative stress, ER stress, heat shock or serum withdrawal.

During viral infection, PKR is transcriptionally induced by interferon but remains latent until it interacts with dsRNA. This interaction induces a conformational …

An Iterative Bézier Method For Fitting Beta-Sheet Component Of A Cryo-Em Density Map, Michael Poteat, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures. We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that …

Retinal Ganglion Cell Neuroprotection Induced By Neuropharmacological Agents In An In-Vivo Model Of Glaucoma, Quinn Ameel

Honors Theses

Recent discoveries from this lab have demonstrated that activation of alpha7 nicotinic acetylcholine receptors (α7 nAChRs) on retinal ganglion cells (RGCs) in the retina is linked to neuroprotection of RGCs that are typically lost in glaucoma-like conditions. Various chemical agents have been produced to increase overall neurotransmission of ACh from cholinergic neurons. DMP-543 is an agent that increases calcium release from cholinergic synaptic terminals. Donepezil is an acetylcholinesterase inhibitor that inhibits the breakdown of ACh in the synaptic cleft, prolonging ACh’s effect. In this study, the neuroprotective activity of these two agents was analyzed at the synapse between starburst amacrine …

The Role Of Nicotine, A7 Nicotinic Acetylcholine Receptors And Extracellular Matrix Remodeling In Pulmonary Fibrosis., Glenn Ward Vicary

Electronic Theses and Dissertations

The median survival for idiopathic pulmonary fibrosis (IPF) patients from diagnosis is a dismal 3 years. This condition is characterized by pulmonary fibroproliferation and excess production and disordered deposition of extracellular matrix (ECM) proteins resulting in obliteration of the original tissue architecture, loss of lung function and eventual death due to respiratory failure. The main hindrance to the development of effective treatments against pulmonary fibrosis is the late detection of its progression and is often of unknown cause. Tobacco smoke represents the most important environmental factor linked to the development of pulmonary fibrosis, with over 60% of IPF patients current …

A Novel Codon-Optimized Siv Gag-Pol Immunogen For Gene-Based Vaccination, Catherine M. Crosby, Eric A. Weaver, Reeti Khare, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Simian immunodeficiency virus (SIV) is a robust pathogen used in non-human primates to model HIV vaccines. SIV encodes a number of potential vaccine targets. By far the largest and most conserved protein target in SIV is its gag-pol protein that bears many epitopes to drive multivalent immune T cell responses. While gag-pol is an attractive antigen, it is only translated after a frame shift between gag and pol with the effect that gag and pol are expressed at an approximate 10/1 ratio. The codon bias of native lentiviral genes are also mismatched with the abundance of tRNAs in mammalian cells …

Immune Monitoring In Recipients Of Combined Living Donor Kidney And Hematopoietic Stem/Facilitating Cell Transplants., Mark Dewayne Badder

Electronic Theses and Dissertations

Solid organ transplantation coupled with a hematopoietic stem cell transplant from the organ donor allows for the recipient to cease immunosuppressive therapy after transplant via a chimeric immune system. This beneficial effect of stem cell transplants is negatively affected by graft versus host disease (GVHD). Better understanding of the donor and recipient’s immune system is vital to mitigating graft versus host disease and induction of donor chimerism without GVHD. In this study, flow cytometry was used to characterize immune cells of the recipients’ before and up to eighteen months post transplantation. The recipients were categorized into their respective chimeric groups. …

The Nucleolar Protein Nucleophosmin Undergoes Liquid-Liquid Phase Separation With Arginine-Rich Nucleolar Proteins Through Weak, Multivalent Electrostatic Interactions, Jaclyn Alicia Cika

Theses and Dissertations (ETD)

Nucleoli are nuclear membrane-less organelles that are the sites for ribosome biogenesis and serve as sensors of cellular stress. Weak, multivalent protein-protein interactions and interactions between disordered, low complexity domains (LCDs) and rRNA have been shown to promote liquid-liquid phase separation (LLPS) in vitro, suggesting a basis for the liquid-like behavior of nucleoli. Nucleophosmin (NPM1), a multifunctional and highly abundant nucleolar protein, exhibits structural features associated with LLPS suggesting a role in nucleolar organization. Specifically, NPM1 forms a pentamer through its N-terminal oligomerization domain and can bind to rRNA through its C-terminal nucleic acid binding domain. Multiple acidic tracts throughout …

Endosomal Trafficking As A Determinant Of Antifungal Tolerance In The Pathogenic Fungus Candida Albicans, Arturo Luis Luna

Theses and Dissertations (ETD)

Several important antifungal drugs inhibit the synthesis of ergosterol, a lipid that modulates the thickness, fluidity and permeability of fungal cell membranes. These include the azole antifungals, which block ergosterol biosynthesis by inhibiting lanosterol demethylase (Erg11p). The resulting depletion of cellular ergosterol and the accumulation of ‘toxic’ sterol intermediates are both thought to cause plasma membrane dysfunction and ultimately growth arrest. However, the effects of ergosterol depletion upon the function of intracellular membranes and organelles are not well described. The purpose of this study was to characterize the effects of azole treatment upon the integrity of the Candida albicans vacuole, …

Seniors Welcome! Avoiding The Trap Of Age Limits In Health Research, Arshad Jahangir

Journal of Patient-Centered Research and Reviews

The guest editor introduces this specialty issue of the Journal of Patient-Centered Research and Reviews, which focuses on cardiovascular diseases in the elderly. The reality of an aging population has increased the need for better evidence-based medicine in older patients. However, randomized controlled trials frequently exclude such patients, especially those with comorbidities, from study. This practice ignores the fact that physiologic changes to the cardiovascular system caused by the aging process and aging-associated diseases create clinical dilemmas distinct from those in younger patients. Considering the rising costs of health care and growing incidence of cardiovascular disease, research efforts and …

Interleukin-17a Promotes Cd8 T Cell Cytotoxicity To Facilitate West Nile Virus Clearance, Amber M. Paul, Dhiraj Acharya, Penghua Wang, Jianfeng Dai, David Gate

Publications

CD8 T cells are crucial components of immunity and play a vital role in recovery from West Nile virus (WNV) infection. Here, we identify a previously unrecognized function of interleukin-17A (IL-17A) in inducing cytotoxic-mediator gene expression and promoting CD8 T cell cytotoxicity against WNV infection in mice. We find that IL-17A-deficient (Il17a/) mice are more susceptible to WNV infection and develop a higher viral burden than wild-type (WT) mice. Interestingly, the CD8 T cells isolated from Il17a/ mice are less cytotoxic and express lower levels of cytotoxic-mediator genes, which can be restored by supplying recombinant IL-17A in vitro and in …